I find File::Copy an excellent reason to use system. Things I cannot do with File::Copy:

1. Preserve the execute bit.
2. Copy more than one file at a time.
3. Recursively copy.
4. Use any of the other arguments of cp.
5. Use scp with a mostly similar syntax as cp for copying to different machines.

Luckely the destructiveness doing of File::Copy::copy("file1", "file2", "dir") has been fixed in 5.12.

I never use File::Copy anymore. I've spend way too much time fighting it. system "cp" never, ever surprises me, and always just works.